Validation Report - gap@1.6
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package gap
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 109 |
| has_vignettes | 10 |
| export_help | 109 |
| has_website | TRUE |
| has_maintainer | Jing Hua Zhao jinghuazhao@hotmail.com |
| bugs_status | 0.4285714 |
| assess_size_codebase | 5521 |
| has_source_control | https://github.com/jinghuazhao/R |
| has_bug_reports_url | 1 |
| downloads_1yr | 140896 |
| reverse_dependencies | 7 |
| has_examples | 1 |
| dependencies | 5 |
| license | GPL (>= 2) |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | gap.datasets (>= 0.0.6) | Depends |
| 2 | dplyr | Imports |
| 3 | ggplot2 | Imports |
| 4 | plotly | Imports |
| 5 | Rdpack | Imports |
Package dependencies
Reverse dependencies
Overall the package has 7 reverse dependencies:
BayesianTools, DHARMa, FamAgg, gaawr2, PopGenReport, pould, rehh
Namespace
Overall the package has 109 exported objects. 109 are documented:
a2g ab
TRUE TRUE
AE3 allele.recode
TRUE TRUE
asplot b2r
TRUE TRUE
BFDP bt
TRUE TRUE
ccsize chow.test
TRUE TRUE
chr_pos_a1_a2 ci2ms
TRUE TRUE
circos.cis.vs.trans.plot circos.cnvplot
TRUE TRUE
circos.mhtplot circos.mhtplot2
TRUE TRUE
cis.vs.trans.classification cnvplot
TRUE TRUE
comp.score cs
TRUE TRUE
ESplot fbsize
TRUE TRUE
FPRP g2a
TRUE TRUE
gc.em gc.lambda
TRUE TRUE
gcontrol gcontrol2
TRUE TRUE
gcp genecounting
TRUE TRUE
geno.recode get_b_se
TRUE TRUE
get_pve_se get_sdy
TRUE TRUE
gif grid2d
TRUE TRUE
h2_mzdz h2.jags
TRUE TRUE
h2G h2GE
TRUE TRUE
h2l hap
TRUE TRUE
hap.control hap.em
TRUE TRUE
hap.score hmht.control
TRUE TRUE
hwe hwe.cc
TRUE TRUE
hwe.hardy hwe.jags
TRUE TRUE
inv_chr_pos_a1_a2 invnormal
TRUE TRUE
ixy KCC
TRUE TRUE
kin.morgan klem
TRUE TRUE
labelManhattan LD22
TRUE TRUE
LDkl log10p
TRUE TRUE
log10pvalue logp
TRUE TRUE
makeped masize
TRUE TRUE
MCMCgrm METAL_forestplot
TRUE TRUE
metap metareg
TRUE TRUE
mht.control mhtplot
TRUE TRUE
mhtplot.trunc mhtplot2
TRUE TRUE
mia miamiplot
TRUE TRUE
miamiplot2 mr
TRUE TRUE
mr_forestplot mtdt
TRUE TRUE
mtdt2 muvar
TRUE TRUE
mvmeta pbsize
TRUE TRUE
pbsize2 pedtodot
TRUE TRUE
pedtodot_verbatim pfc
TRUE TRUE
pfc.sim pgc
TRUE TRUE
pvalue qqfun
TRUE TRUE
qqunif qtl2dplot
TRUE TRUE
qtl2dplotly qtl3dplotly
TRUE TRUE
qtlClassifier qtlFinder
TRUE TRUE
read.ms.output ReadGRM
TRUE TRUE
ReadGRMBin revStrand
TRUE TRUE
runshinygap s2k
TRUE TRUE
sentinels snptest_sample
TRUE TRUE
tscc whscore
TRUE TRUE
WriteGRM WriteGRMBin
TRUE TRUE
xy
TRUE Examples
There are 116 help pages with examples, from 116 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.2 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-03-19 03:32:58 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.3 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.50 jsonlite_1.9.1
[10] xfun_0.51 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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FALSE
ACCEPT_EULA Y
ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE
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ANDROID_NDK_LATEST_HOME
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ANDROID_SDK_ROOT /usr/local/lib/android/sdk
ANT_HOME /usr/share/ant
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BOOTSTRAP_HASKELL_NONINTERACTIVE
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GITHUB_TRIGGERING_ACTOR
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GOROOT_1_23_X64 /opt/hostedtoolcache/go/1.23.7/x64
GRADLE_HOME /usr/share/gradle-8.13
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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LN_S ln -s
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NVM_DIR /home/runner/.nvm
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_LIMIT 100
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
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PIPX_HOME /opt/pipx
PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_BIN_PATH /opt/quarto/bin
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
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R_DOC_DIR /opt/R/4.4.3/lib/R/doc
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R_PLATFORM x86_64-pc-linux-gnu
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SED /usr/bin/sed
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SGX_AESM_ADDR 1
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SWIFT_PATH /usr/share/swift/usr/bin
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TAR /usr/bin/tar
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
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$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
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else {
cli_server_default(msg)
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}
<bytecode: 0x5558b083d330>
<environment: namespace:cli>
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<bytecode: 0x5558afe14cd8>
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$rl_word_breaks
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$rlang_trace_top_env
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$scipen
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$str$list.len
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$str$formatNum
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$try.outFile
A connection with
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